Contacts of the strand formed by residues 179 - 184 (chain E) in PDB entry 1ACB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 179 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100E ASN* 3.3 20.7 + - - +
101E ASN* 3.6 24.4 + - - +
177E LYS 3.3 1.2 - - - -
178E ASP* 1.3 75.9 - - + +
180E MET* 1.4 61.4 - - - +
229E ALA* 3.6 9.0 - - - +
230E ARG* 3.0 21.3 + - - -
233E ALA* 4.1 22.9 - - + -
234E LEU* 4.3 9.1 - - + +
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Residues in contact with MET 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E THR 3.4 25.1 - - - +
99E ILE 3.7 16.2 - - - +
100E ASN* 3.8 11.9 - - + +
165E ASN* 3.4 10.4 + - - -
175E LYS 3.3 18.4 - - - +
176E ILE* 3.7 9.4 - - + -
177E LYS* 3.2 41.5 - - + +
178E ASP 3.0 0.8 - - - -
179E ALA* 1.4 84.9 - - - +
181E ILE* 1.3 62.0 + - - +
215E TRP* 3.8 9.9 - - - +
227E VAL* 3.7 23.8 - - + -
228E TYR 3.2 6.3 - - - +
229E ALA* 5.6 1.1 - - - -
230E ARG* 3.2 22.2 + - - -
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Residues in contact with ILE 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E PHE* 5.1 4.3 - - + +
162E LEU* 4.0 29.8 - - + -
163E LEU 4.5 8.3 - - - +
165E ASN* 4.4 1.8 - - - +
180E MET* 1.3 77.1 - - - +
182E CYS* 1.3 73.6 + - - +
199E LEU* 5.0 3.4 - - + -
210E VAL* 4.1 22.4 - - + +
211E GLY* 4.4 2.0 - - - -
227E VAL* 4.5 0.2 - - - -
228E TYR* 2.6 56.3 + - + +
230E ARG* 3.7 49.6 - - + +
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Residues in contact with CYS 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E LEU* 3.6 2.3 - - - +
163E LEU* 2.8 39.5 + - + +
165E ASN* 4.7 3.7 + - - -
168E CYS* 2.0 52.9 - - + -
176E ILE* 4.0 20.2 - - - -
181E ILE* 1.3 86.4 - - - +
183E ALA* 1.3 64.3 + - - +
225E PRO* 4.1 1.1 - - + -
226E GLY 3.3 12.3 - - - +
227E VAL* 4.1 4.7 - - - -
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Residues in contact with ALA 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E LEU* 4.3 8.6 - - + +
161E PRO 3.2 9.4 - - - +
162E LEU* 4.2 16.4 - - + -
163E LEU* 2.9 10.5 - - - +
181E ILE* 6.5 0.2 - - + -
182E CYS* 1.3 78.4 - - - +
184E GLY* 1.3 65.0 + - - +
199E LEU* 4.3 11.4 - - + -
225E PRO* 3.6 0.2 - - - +
226E GLY* 3.0 29.3 + - - -
228E TYR* 3.7 22.5 + - + -
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Residues in contact with GLY 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E LEU* 4.0 13.6 - - - +
161E PRO* 2.8 24.3 + - - +
163E LEU* 3.6 6.4 - - - +
183E ALA* 1.3 80.8 - - - +
185E ALA* 1.3 72.9 + - - +
186E SER* 2.9 18.2 + - - -
188E VAL* 5.1 4.5 - - - -
225E PRO* 4.3 0.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il